Hi everyone! Wondering if there are any plans to implement a function in scanpy that would filter “empty droplets” containing cells, like EmptyDrops (https://www.biorxiv.org/content/10.1101/234872v2) or SoupX (https://www.biorxiv.org/content/10.1101/303727v1)? Or really anything more advanced than just setting a fixed cutoff for counts/genes per cell?
I guess empty droplets is now pretty much incorporated already into Cell Ranger v3, so this would hopefully happen at an earlier stage. You are completely right that SoupX, on the other hand, would be a great addition to scanpy external. We would have to reach out to them to see if they are interested in integrating this into scanpy. I will put it on the list